In Blended Learning, students receive a combination of traditional face to face instruction in class and are also required to complete activities outside of the classroom. BL increases opportunities for faculty members to design more effective teaching and learning environments. In order to do so, Instructional Design might be used to support blended courses planning and management. This study has investigated the simultaneous implementation of 38 blended courses in a private Brazilian university, which involved more than 11,000 students and 250 teachers. The general objective of this study was to assess whether instructional design and course management practices as well as interaction affect students' instruction. Through the use of Structural Equation Modeling, this study found out that instructional design positively influences instruction, especially when mediated by interaction. This study did not find a significant effect of course management over instruction. This study presents some implications to instructional designers and teachers of blended courses.